Thanks to the ideas on this thread! Although I didn't post, I used it as a reference for our stay in Cairns earlier this week. Here is what we did:
* Sunday: arrival, explore town, dinner at a small pub
* Monday: Sky Rail/Sky Train, lunch and explored Kuranda (there was a crepe place that was really good)
* Tuesday: day on the reef. we ended up at a place that had its own place docked. I did snuba and a, "snorkel safari." both were excellent, and they took some great underweater photos.
* Wednesday: drove up to Daintree. the drive is amazing!
* Thursday: just went to the Botanic Gardens before flying out. they were surprisingly good, and free

Along with those, I swim and found the Tobruk Memorial Pool, which is one of the best pools (in the world) that I've ever been in. 50m, 10 lanes, and I had my own lane most of the time. It was about a 5-10 min drive from our hotel.

We had dinner at the aquarium once, which was also a great experience. Supposedly if you want a table beside the aquarium you need to book a week out, but we sat outside and were still able to see it, and get the fresh air.